Identification of loci for cold tolerance at reproductive stage and seed shattering in Ethiopian rice cultivar ‘X-Jigna’

Genetic improvement is essential for improved rice production in the high-elevation, cool-climate regions of Ethiopia. We conducted QTL-seq analysis using 846 RIL F5 populations of ‘X-Jigna’, a dominant rice cultivar in Ethiopia, × ‘Hitomebore’, a cold-tolerant elite Japanese cultivar, in field trials in Japan. We detected three QTLs for cold tolerance for inducing spikelet sterility under cold at reproductive stage (qSFC5, qSFC8, and qSFC10) and one for seed shattering habit (qSHT1). In haplotype analysis using indel markers in an F6 population in Japan and Ethiopia, qSFC5 and qSFC8 were confirmed in Japan and qSHT1 was confirmed in both Japan and Ethiopia. Markers for the cold tolerance and seed shattering will be useful to speed up breeding in Ethiopia.